Results for “ssl”

Annotate CLIP-seq peaks or crosslink sites to RNA features (5'UTR, CDS, 3'UTR, intron, splice junction, snoRNA, tRNA, ncRNA, repeat elements) with ChIPseeker, RCAS, RBP-Maps (Yeo splicing regulatory maps), and bedtools, applying feature-priority hierarchies, transcript-context resolution, and metagene aggregation. Use when characterizing where in transcripts an RBP binds, comparing peak distribution across regions, generating splicing-regulatory maps relative to alternative-splicing events, or distinguishing exonic vs intronic vs UTR binding.

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Identify differentially bound regions across CLIP-seq conditions (knockdown vs control, treatment vs vehicle, disease vs healthy) using DEWSeq (sliding-window DESeq2), Flipper (Skipper-downstream), ASpeak, edgeR, or limma-voom. Use when computing condition-level changes in RBP binding intensity, choosing peak-level vs window-level vs crosslink-level testing, designing replicate experiments, or distinguishing biological binding shifts from technical confounders.

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Profiles RNA-binding protein targets without antibody or UV crosslinking using STAMP (APOBEC1-RBP fusion, C-to-U editing), scSTAMP (single-cell), TRIBE/HyperTRIBE (ADAR-RBP, A-to-I editing), DART-seq (APOBEC1-YTH for m6A), or Bullseye/SAILOR edit-site detection pipelines. Use when antibody is unavailable or specificity is doubtful, when single-cell RBP profiling is needed (scSTAMP), or when in vivo RBP profiling without UV is preferred.

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Provides patterns to configure AWS RDS (Aurora, MySQL, PostgreSQL) with Spring Boot applications. Configures HikariCP connection pools, implements read/write splitting, sets up IAM database authentication, enables SSL connections, and integrates with AWS Secrets Manager. Use when setting up RDS connections in Spring Boot, configuring connection pooling, or managing database credentials securely.

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Grill the user relentlessly about a plan, decision, or idea. Use when the user wants to stress-test their thinking, or uses any 'grill' trigger phrases ("grill me", "grill with docs").

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Find and fix WCAG 2.2 accessibility issues. Two modes — report (sweep a codebase or page, produce a prioritized written report, no edits) and fix (audit→edit→verify loop on a target). Prefers direct-CDP live-DOM auditing; falls back to a browser-MCP composition or HTML-string audits.

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Audit a live page for accessibility issues, locate each WCAG violation precisely, and return a selector-grounded fix worklist without editing.

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Diff a live page's accessibility violations against a baseline — by default compares uncommitted changes (stash-based), or pass --branch [<name>] to diff against a branch. Reports only new violations introduced, violations fixed, and pre-existing count. Use `scan` for a full audit with no diffing.

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Extract study sites, observational variables, coordinates, climate-forcing sources, and cited data sources from ecosystem-modeling papers, PDFs, supplements, or article text, then plan or create EcoSIM simulation workflows and run folders for those sites. Use when Codex is asked to read a paper for EcoSIM feasibility, including requests phrased as "read paper for ecosim feasibility"; read a paper for sites/data availability; reproduce a published site simulation in EcoSIM; compare EcoSIM outputs to paper observations; or convert paper-derived AmeriFlux, FLUXNET, US NLDAS-domain, non-US ERA5, crop, peatland, forest, grassland, wetland, or unmanaged field-site information into EcoSIM inputs and runnable cases.

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Passive domain reconnaissance using Python stdlib. Subdomain discovery, SSL certificate inspection, WHOIS lookups, DNS records, domain availability checks, and bulk multi-domain analysis. No API keys required.

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Fast tokenizers optimized for research and production. Rust-based implementation tokenizes 1GB in <20 seconds. Supports BPE, WordPiece, and Unigram algorithms. Train custom vocabularies, track alignments, handle padding/truncation. Integrates seamlessly with transformers. Use when you need high-performance tokenization or custom tokenizer training.

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Configuração e diagnóstico de Nginx — reverse proxy, TLS, HTTP/2, HTTP/3, cache, compressão, rate limit e load balancing. Use quando o usuário disser "nginx", "reverse proxy", "502", "504", "certificado", "SSL", "TLS", "rate limit", "cache", "upstream".

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Interview the user relentlessly about a plan or design until reaching shared understanding, resolving each branch of the decision tree. Use when user wants to stress-test a plan, get grilled on their design, or mentions "grill me".

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Profiles RNA-binding protein targets without antibody or UV crosslinking using STAMP (APOBEC1-RBP fusion, C-to-U editing), scSTAMP (single-cell), TRIBE/HyperTRIBE (ADAR-RBP, A-to-I editing), DART-seq (APOBEC1-YTH for m6A), or Bullseye/SAILOR edit-site detection pipelines. Use when antibody is unavailable or specificity is doubtful, when single-cell RBP profiling is needed (scSTAMP), or when in vivo RBP profiling without UV is preferred.

The English summary is being prepared. Showing the original description.

Annotate CLIP-seq peaks or crosslink sites to RNA features (5'UTR, CDS, 3'UTR, intron, splice junction, snoRNA, tRNA, ncRNA, repeat elements) with ChIPseeker, RCAS, RBP-Maps (Yeo splicing regulatory maps), and bedtools, applying feature-priority hierarchies, transcript-context resolution, and metagene aggregation. Use when characterizing where in transcripts an RBP binds, comparing peak distribution across regions, generating splicing-regulatory maps relative to alternative-splicing events, or distinguishing exonic vs intronic vs UTR binding.

The English summary is being prepared. Showing the original description.

Identify differentially bound regions across CLIP-seq conditions (knockdown vs control, treatment vs vehicle, disease vs healthy) using DEWSeq (sliding-window DESeq2), Flipper (Skipper-downstream), ASpeak, edgeR, or limma-voom. Use when computing condition-level changes in RBP binding intensity, choosing peak-level vs window-level vs crosslink-level testing, designing replicate experiments, or distinguishing biological binding shifts from technical confounders.

The English summary is being prepared. Showing the original description.

Preprocess CLIP-seq reads (eCLIP, iCLIP, iCLIP2, iCLIP3, irCLIP, PAR-CLIP, FLASH) with protocol-specific UMI extraction, adapter trimming, length filtering, and post-alignment PCR-duplicate collapse. Use when raw CLIP FASTQ must be turned into deduplicated, crosslink-preserving BAM input for peak calling; choosing between two-pass and single-pass adapter trimming; deciding minimum read length; or mapping UMI patterns to specific eCLIP/iCLIP/iCLIP2/iCLIP3 library preps.

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Call protein-RNA binding sites from CLIP-seq BAM with CLIPper, PureCLIP, Skipper, Piranha, omniCLIP, CTK, CLAM, or Paraclu. Use when choosing between coverage-based, HMM-based, beta-binomial window-based, and crosslink-site-based peak callers; applying ENCODE eCLIP thresholds (log2 IP/SMInput >= 3, -log10 p >= 3); deciding when SMInput is mandatory; or reconciling peak-set discordance between callers for the same RBP.

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Audit codebases and infrastructure for security issues. Use when scanning dependencies for vulnerabilities, detecting hardcoded secrets, checking OWASP top 10 issues, verifying SSL/TLS, auditing file permissions, or reviewing code for injection and auth flaws.

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Audit codebases, infrastructure, AND agentic AI systems for security issues. Covers traditional security (dependencies, secrets, OWASP web top 10, SSL/TLS, file permissions) PLUS agentic security (prompt injection scanning, identity spoofing detection, memory poisoning checks, multi-agent communication audit, OWASP Agentic Top 10). Use when scanning for vulnerabilities, detecting hardcoded secrets, reviewing agent workspace configuration, checking prompt injection vectors, or auditing agent permissions and boundaries.

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Automatically issue/renew HTTPS certificates using Alibaba Cloud ESA DNS + acme.sh (including wildcard *.example.com + example.com), with optional installation to Nginx. Trigger this skill when the user mentions ESA, ATrustDNS, _acme-challenge, acme.sh, Let's Encrypt, No TXT record found, InvalidRecordNameSuffix, wildcard certificate, or Nginx certificate configuration.

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Fast tokenizers optimized for research and production. Rust-based implementation tokenizes 1GB in <20 seconds. Supports BPE, WordPiece, and Unigram algorithms. Train custom vocabularies, track alignments, handle padding/truncation. Integrates seamlessly with transformers. Use when you need high-performance tokenization or custom tokenizer training.

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Passive domain reconnaissance using Python stdlib. Subdomain discovery, SSL certificate inspection, WHOIS lookups, DNS records, domain availability checks, and bulk multi-domain analysis. No API keys required.

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Calendly scheduling integration. List events, check availability, manage meetings via Calendly API.

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